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Studying Legume Genomics

Understanding the genetic makeup of food crops is critical if we want to develop sustainable ways of protecting those crops against disease. To this end, researchers are using genomics to study plants and their characteristics. Distinguished McKnight Professor Nevin Young ( Plant Pathology ),...

Fighting Prostate Cancer

Among different types of cancers, prostate cancer has the highest incidence rate among men, and the second-highest death rate. In early stages of prostate cancer, radiation and surgical resection represent the standard of care, and often lead to good outcomes. In advanced cases, various forms of...

Mesabi Dedication and 2015 Research Exhibition

On Thursday, April 23, MSI held the sixth annual MSI Research Exhibition and dedicated our newest supercomputer, Mesabi . Mesabi is an HP distributed cluster featuring a large number of nodes with leading-edge Intel processors that are tightly integrated via a very high speed communication network...

Simulations in Chemical and Condensed Matter Physics

Abstract: 

Simulations in Chemical and Condensed Matter Physics

This group studies a variety of complex many body systems providing insight at many length and time scales into the collective phenomena of interest. A current focus is on abstracted models of interacting polymer systems far from equilibrium in which they are accumulating data on the statisitcal distribution of chemical morphologies and dynamics. These models are intended to provide better understanding of how dynamic metastable states  involving large molecules can emerge from a starting configuration of small molecules as is believed to have occurred in the origin of life. The researchers have studied a "well mixed reactor" version of such a model and are currently studying an extension in which spatial heterogeneity and diffusion can occur. Studies of the detailed morphological and dynamic character of the well mixed model also continue.  Simulations using more chemically realistic descriptions of the atomic level are also planned.

A second focus is on the behavior of  oxide water interfaces using in-house self consistent tightbinding codes. There is tremendous current interest  in oxides as electrodes in a variety of technologies using aqueous electrolytes including fuel cells, batteries and electrolysers. Water-oxide interfaces are also a key component in corroding metal surfaces so such studies are also relevant to attempts to understand and inhibit corrosion. In one project the researchers are simulating at titania water interfaces with particular emphasis on new methods for calculating surface energies to understand the propensity of titania water interfaces to dissociate water. This project is a collaboration with former student Patrick Schelling, now an associate professor at the University of Central Florida, and his students. A second project in this category is a simulation of the magnetite water interface. In addition to its obvious corrosion relevance, the study is intended to provide better understanding of the mechanisms of water dissociation at a magnetite water interface, as occurs in experiments which the group is doing on the use of magnetite electrodes in electrolysers for production of gaseous hydrogen as an energy storage medium. This project is a collaboration with Professor Melissa Eblen of the Carleton College Physics Department, the Natural Resources Research Institute in Duluth, and high school physics teacher Jon Huber, who worked with the Halley Group in the Research Experiences for Teachers program at Minnesota in summer 2015 and continues experiments with students in Burnsville. In a third related project the researchers are beginning molecular dynamics simulations of membrane proteins in water at various solid aqueous interfaces. The aim is to  explore the possible use of such membrane proteins to solve certain technical problems associated with the behavior of lithium-based electrodes in water in applications to batteries. This is a preliminary exploratory collaboration with Jonathan Sachs of the Department of Biomedical Engineering.

Thirdly the group simulates quantum fluid phenomena. A current emphasis is on condensate mediated transmission using Diffusion Monte Carlo methods to obtain informaton about excited scattering states in the  strongly interacting helium four superfluid. The methods are unique and were developed in this group. They have published results in Physical Review B using a guiding wave function which did not conserve particle current. The current project is to use an improved guiding wave function which removes that defect. The project is relevant to an experiment they proposed more than a decade ago and which has been tried in various laboratories, still without a definitive result, to observe the condensate mediated transmission effect. Another quantum fluids project, carried on at a low intensity level, is the exploration of effects of disorder, and in particular of disorder induced pairing, in superconductors.

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Group name: 
halleyjw

Modeling Variability in the Earth System: From Rainfall, to River Networks, to Landscape Processes

Abstract: 

Modeling Variability in the Earth System: From Rainfall, to River Networks, to Landscape Processes

This research group focuses on a wide range of environmental problems including inverse problems for precipitation estimation from space, stochastic theories of water/sediment transport and landscape evolution, river delta network topology and dynamics for vulnerability assessment, and river morphodynamics from satellite imagery.

Current work focuses on new and innovative formalisms for inverse estimation problems (downscaling, data fusion, retrieval, and data assimilation) of precipitation using multi-sensor, multi-scale measurements from space. New methodologies for quantifying the stochastic nature of bedload sediment transport using multi-scale analysis and dynamical system theory are studied as well. The researchers seek to understand the relations between near-bed turbulence, riverbed morphodynamics, and sediment transport using experimental, theoretical, and numerical approaches. Landscape reorganization under climate change is also studied using both controlled laboratory experiments and conceptual modeling. Dynamical frameworks for the analysis of river meandering dynamics, inferring process from form, and quantifying response to perturbations are further studied in the group. They explore quantitative frameworks for studying river delta topology and dynamics based on graph-theoretic approaches, where deltaic systems are represented by rooted directed acyclic graphs. They also work on developing metrics that capture unique physical, topological, and dynamical aspects of delta networks with the ultimate objective that deltas can be compared and contrasted and also analyzed for relative vulnerability (or resilience) to change. At the basin scale, the researchers investigate network-based frameworks for identifying potential synchronizations and amplifications of sediment delivery to basin outlets and also for identifying hotspots of fluvial geomorphic change based on dynamic connectivity. They also analyze the transport and mixing of water particles traveling in a river basin based on a stochastic Lagrangian formulation of transport to evaluate the residence time distributions, which are fundamental catchment descriptors blending key information about storage, geochemistry, flow pathways, and sources of water into a coherent mathematical framework.

The group has recently begun a campaign to map and analyze river morphodynamics in South America using Landsat imagery. In order to map migration rates for thousands of kilometers of major rivers, they have developed a nearly-automated process that extracts binary water masks from tropical rivers via an in-house supervised classifier that exploits all bands available from Landsat. A toolbox has been developed to process these binary masks to extract river banklines, centerlines, and widths at the pixel (30 m) scale to quantify migration dynamics within the most active channels in the world at an annual timescale for more than three decades. Tools for geomorphologic analysis have been developed that compute migration rates, analyze in-channel bar morphologies, and automatically delineate individual bends through time. These tools are scalable and parallelizable; a proof-of-concept was successfully performed on 1,600 km of the Ucayali River (roughly 50 Landsat scenes). Expanding this study to the entire Amazon region will require computationally intensive processing, hence having access to powerful computational resources and parallel computational capacity is essential for the efficient implementation of these researches.

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Group name: 
foufoula

MSI Supporting DOE Grants in Computational Chemistry

MSI is proud to spotlight some of our researchers in a new series of articles that are aimed both at highlighting their research and illustrating how MSI facilitates it. Christopher Cramer’s group uses supercomputing resources to push the limits of present-day computational chemistry tools in order...

How do I use Globus to transfer data at MSI?

The University of Minnesota participates in the Globus data transfer service. Globus is a service that allows for fast transfer of data between computer systems, using a convenient web interface. Globus data transfer speeds are typically significantly faster than data transfer speeds using other...

ABAQUS

Software Description: 

ABAQUS is a general-purpose Finite Element program designed for advanced linear and nonlinear engineering analysis applications.

The Institute has ABAQUS/Standard, ABAQUS/Explicit and ABAQUS/Cae.

ABAQUS/Standard , provides ABAQUS analysis technology to solve traditional implicit finite element analyses, such as static, dynamics, and thermal, all powered with the widest range of contact and nonlinear material options. ABAQUS/Standard also has optional add-on and interface products with address design sensitivity analysis, offshore engineering, and integration with third party software, e.g., plastic injection molding analysis.

ABAQUS/Explicit , provides ABAQUS analysis technology focused on transient dynamics and quasi-static analyses using an explicit approach appropriate in many applications such as drop test, crushing and many manufacturing processes.

ABAQUS/CAE , provides a complete modeling and visualization environment for ABAQUS analysis products. It provides an access to CAD models, advanced meshing and visualization.

 

Isight is an open-desktop solution used to combine multiple cross-disciplinary models and applications together in a simulation process flow, automate their execution, explore the resulting design space, and identify the optimal design parameters subject to required constraints.

 

Tosca Structure is a flexible, modular software system for non-parametric structural optimization with industry standard finite element solvers (Abaqus, ANSYS, MSC Nastran). Model parameterization is not necessary. Existing solver input files are used for the optimization. Tosca Structure provides advanced capabilities for optimization with nonlinear analysis and fatigue as well as a specific non-parametric morphing approach.

 

Tosca Fluid is a unique, modular software system for non-parametric fluid flow optimization that enables topology optimization with some industry-standard CFD solvers. Abaqus/CFD is not currently supported.

 

fe-safe is fatigue analysis software for Finite Element models that offers its users the most accurate and advanced fatigue analysis technology for real-world industrial applications. fe-safe is used by leading companies in automotive, heavy truck, off-highway, marine, defense, offshore, power generation, wind energy, medical engineering and many other industries.

Software Support Level: 
Secondary Support
Software Access Level: 
Limited Licenses
Citrix Documentation: 

To run this software under Windows, connect using the instructions provided in our Windows systems page. Once logged in, navigate to:

Start > All Programs > Abaqus 6.13-2

Notes


  • In order to allow all users access to Abaqus, users are allowed to have 2 Abaqus jobs running at one time. If licenses are available, users may run more than 2 jobs. But, for each user, all jobs beyond the 2 job limit are subject to being killed if licenses are needed by other users. The user's most recently started job will be killed first.
  • You must be on the Abaqus users list to run Abaqus. Contact help@msi.umn.edu to be added to the Abaqus users list.
  • Abaqus sometimes has graphical interface issues with the menus and tool bars not being displayed properly. If you run into this issue and are using KDE or GNOME, please try using a different Desktop Manager such as FVWM, ICEWM and MWM.
  • If you would prefer not to change your desktop manager then do the following:

     1. right click on the top bar of your abaqus window
    
     2. choose Configure window behavior 
    
     3. under Compositing State, click on Suspend Compositing
    
    
  • To submit a job in the queue, it is essential to have the keyword interactive next to the ABAQUS command line in the submission script, see the above example.
  • To run from the /scratch file systems, add the following line to the abaqus_v6.env:

    scratch="/scratch/directoryname"
    
    or
    
    scratch="/scratch1/directoryname"
    
    

    Where directoryname is the name of the directory you want to use as a scratch directory for temporary data storage.

  • ABAQUS CAE cannot use hardware graphics acceleration in Apple's X11. To run CAE on a Macintosh, use the -mesa option to disable hardware acceleration:

    module load abaqus
    abaqus cae -mesa
    

    Depending on the graphics drivers on your local computer, in order to run ABAQUS CAE over a remote connection, other non-Apple clients may also need to use the "-mesa" option. Note that this is an unsupported configuration and performance will be slow.

The manuals are only available on the MSI network: https://wwwr.msi.umn.edu/abaqus/Documentation/docs/

PBS Example: 

Programs can be submitted to a queue using PBS script such as the one below.:

#PBS -l nodes=1:ppn=1,mem=1gb,walltime=4:00:00

#PBS -m abe

module load abaqus

abaqus job=job_name input=data.inp interactive 
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment use the commands:

module load abaqus 
abaqus cae

or

module load abaqus 
abaqus job=job_name inp=input interactive

Programs can be submitted to a queue using PBS script such as the one below.:

#PBS -l nodes=1:ppn=1,mem=1gb,walltime=4:00:00
#PBS -m abe

module load abaqus
abaqus job=job_name input=data.inp interactive 

Notes


  • In order to allow all users access to Abaqus, users are allowed to have 2 Abaqus jobs running at one time. If licenses are available, users may run more than 2 jobs. But, for each user, all jobs beyond the 2 job limit are subject to being killed if licenses are needed by other users. The user's most recently started job will be killed first.
  • You must be on the Abaqus users list to run Abaqus. Contact help@msi.umn.edu to be added to the Abaqus users list.
  • Abaqus sometimes has graphical interface issues with the menus and tool bars not being displayed properly. If you run into this issue and are using KDE or GNOME, please try using a different Desktop Manager such as FVWM, ICEWM and MWM.
  • If you would prefer not to change your desktop manager then do the following:

     1. right click on the top bar of your abaqus window
    
     2. choose Configure window behavior 
    
     3. under Compositing State, click on Suspend Compositing
    
    
  • To submit a job in the queue, it is essential to have the keyword interactive next to the ABAQUS command line in the submission script, see the above example.
  • To run from the /scratch file systems, add the following line to the abaqus_v6.env:

    scratch="/scratch/directoryname"
    
    or
    
    scratch="/scratch1/directoryname"
    
    

    Where directoryname is the name of the directory you want to use as a scratch directory for temporary data storage.

  • ABAQUS CAE cannot use hardware graphics acceleration in Apple's X11. To run CAE on a Macintosh, use the -mesa option to disable hardware acceleration:

    module load abaqus
    abaqus cae -mesa
    

    Depending on the graphics drivers on your local computer, in order to run ABAQUS CAE over a remote connection, other non-Apple clients may also need to use the "-mesa" option. Note that this is an unsupported configuration and performance will be slow.

The manuals are only available on the MSI network: https://wwwr.msi.umn.edu/abaqus/Documentation/docs/

UofM Receives Funding From NSF for Dedicated Campus Research Network

The University of Minnesota today announced the National Science Foundation (NSF) has awarded it $500,000 to build a dedicated research and computing network enabling researchers on its Twin Cities campus to more easily collaborate and innovate with research institutions around the world in their...

Galaxy

The Galaxy web application is an integrated informatics solution that supports both data analysis and research discovery. It is useful to beginning, intermediate and advanced informatics users or researchers alike. Skills/Software Needed: Galaxy is a web-based application that can be used from any...

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